docs: def apply(self, configuration, schema, args):
          """
          Apply the plugin to the configuration.
  
          Inheriting plugins should implement this method to add additional functionality.
  
          Parameters
          ----------
          configuration : dict
              configuration
          schema : dict
              JSON schema
          args : argparse.NameSpace
              parsed command line arguments
  
          Returns
          -------
          configuration : dict
              updated configuration after applying the plugin
          """
          # Set values from the command line
          for name, path in self.arguments.items():
              value = getattr(args, name.replace('-', '_'))
              if value is not None:
                  util.set_value(configuration, path, value)
  
          return configuration